Protein-Protein interaction for Upregulated genes

Question

[1961012]

I am doing Protein-Protein interaction Network analysis for DEGs using string but I am getting huge network even When using high confidence score of interaction = 0.7.

my goal is to determine hub proteins in a pathological condition. can I consider the upregulated genes only ??

thank you in advance!!

Answer 1

[Mensur Dlakic]

What exactly is a huge network? I have looked at networks with thousands of proteins in Cytoscape and was still able to find hub proteins, though admittedly it is easier to do so with smaller networks.

There are some interesting comments on the right-hand side of this page where it says Similar posts.

We also had a similar discussion here. Sometimes people take more strict significance thresholds because otherwise they get more data to analyze than what they would like. In your case, taking a smaller p-value or larger fold-change cutoffs would eventually give you a smaller network in Cytoscape. Similarly, taking a higher interaction confidence score in Cytoscape (say, 0.8-0.9) would give you a smaller network. I think both of those are better solutions than looking at upregulated genes only.

As already explained in one of those posts on the right, I would suggest to take a 0.9 confidence score and use that network for visualization because it will be easier to explain when you have an audience or someone who doesn't want to look for details. However, I would still look at a larger network for additional proteins that may not be present in high-confidence network.